title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1910 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The identification of immune genes in the milk transcriptome of the Tasmanian devil (Sarcophilus harrisii) link: https://peerj.com/articles/1569 last-modified: 2016-01-12 description: Tasmanian devil (Sarcophilus harrisii) pouch young, like other marsupials, are born underdeveloped and immunologically naïve, and are unable to mount an adaptive immune response. The mother’s milk provides nutrients for growth and development as well as providing passive immunity. To better understand immune response in this endangered species, we set out to characterise the genes involved in passive immunity by sequencing and annotating the transcriptome of a devil milk sample collected during mid-lactation. At mid-lactation we expect the young to have heightened immune responses, as they have emerged from the pouch, encountering new pathogens. A total of 233,660 transcripts were identified, including approximately 17,827 unique protein-coding genes and 846 immune genes. The most highly expressed transcripts were dominated by milk protein genes such as those encoding early lactation protein, late lactation proteins, α-lactalbumin, α-casein and β-casein. There were numerous highly expressed immune genes including lysozyme, whey acidic protein, ferritin and major histocompatibility complex I and II. Genes encoding immunoglobulins, antimicrobial peptides, chemokines and immune cell receptors were also identified. The array of immune genes identified in this study reflects the importance of the milk in providing immune protection to Tasmanian devil young and provides the first insight into Tasmanian devil milk. creator: Rehana V. Hewavisenti creator: Katrina M. Morris creator: Denis O’Meally creator: Yuanyuan Cheng creator: Anthony T. Papenfuss creator: Katherine Belov uri: https://doi.org/10.7717/peerj.1569 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hewavisenti et al. title: The influence of mature oak stands and spruce plantations on soil-dwelling click beetles in lowland plantation forests link: https://peerj.com/articles/1568 last-modified: 2016-01-12 description: Most European forests have been converted into forest plantations that are managed for timber production. The main goal of this paper was to determine the difference between mature native sessile oak (Quercus petraea) stands and non-indigenous Norway spruce (Picea abies) plantations, with respect to communities of Athous click beetles in approximately 6,500 ha of lowland plantation forest area in the Czech Republic. Athous subfuscus was the most abundant and widespread species, followed by A. zebei and A.haemorrhoidalis, while A. vittatus was considered rare. Spatial analysis of environmental variables inside studied patches showed that the species composition of Athous beetles best responded to a 20 m radius surrounding traps. The species’ responses to the environment showed that A. vittatus and A. haemorrhoidalis preferred oak stands, while A. zebei and A. subfuscus were associated with spruce plantations. In addition, oak stands showed higher diversity of beetle communities. The studied species are important for their ecosystem services (e.g. predation on pests or bioturbation) and seem to tolerate certain degrees of human disturbances, which is especially beneficial for forest plantations managed for timber production. creator: Tereza Loskotová creator: Jakub Horák uri: https://doi.org/10.7717/peerj.1568 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Loskotová & Horák title: Validation of the “Quality of Life in School” instrument in Canadian elementary school students link: https://peerj.com/articles/1567 last-modified: 2016-01-12 description: Background. School is an integral component of the life of a child, and thus quality of school life is an important part of the overall quality of life experienced by a child. There are a few instruments available to measure the quality of school life but they are often not available in English, or they are not appropriate for use alongside other instruments in a survey of young children. The Quality of Life in School (QoLS) instrument is a short, self-report measure to assess elementary school students’ perception of their quality of school life in four domains. The instrument was developed in Israel and has been validated among Hebrew-speaking children. The aim of the current study was to evaluate the psychometric properties of the QoLS measure in Canadian elementary school children.Methods. A total of 629 children attending grades 4–6 were recruited in a population-based cross-sectional study. The QoLS measure was administered to participating children by trained research assistants. In addition, their socio-demographic details and academic data were also obtained. The psychometric testing included exploratory factor analysis and reliability estimation using internal consistency (Cronbach’s Alpha). Construct validity was investigated using the known groups comparisons for discriminative validity and via convergent validity.Results. A four-factor structure was generated explaining 39% of the total variance in the model. The results showed good internal consistency and acceptable floor and ceiling effects. Cronbach’s Alpha ranged from 0.75 to 0.93. Known groups comparisons showed that the QoLS measure discriminated well between subgroups on the basis of gender, grade, and academic achievement, thus providing evidence of construct validity. The convergent validity was also appropriate with all the four domains demonstrating moderate to strong correlations to each other and to the total QoLS score.Conclusions. QoLS appears to be a valid and reliable measure for quality of school life assessment in young Canadian children. creator: Satvinder Ghotra creator: Jessie-Lee D. McIsaac creator: Sara F.L. Kirk creator: Stefan Kuhle uri: https://doi.org/10.7717/peerj.1567 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ghotra et al. title: Characterization of the artisanal fishing communities in Nepal and potential implications for the conservation and management of Ganges River Dolphin (Platanista gangetica gangetica) link: https://peerj.com/articles/1563 last-modified: 2016-01-12 description: The Ganges River dolphin (Platanista gangetica gangetica) (GRD) is classified as one of the most endangered of all cetaceans in the world and the second scarcest freshwater cetacean. The population is estimated to be less than 2,000 individuals. In Nepal’s Narayani, Sapta Koshi, and Karnali river systems, survival of GRD continues to be threatened by various anthropogenic activities, such as dam construction and interactions with artisanal fisheries. A basic description of the geographic scope, economics, and types of gear used in these fisheries would help managers understand the fishery-dolphin interaction conflict and assist with developing potential solutions. The main goal was to provide new information on the artisanal fishing communities in Nepal. The specific objectives were to identify, compile, and investigate the demographics, economics, fishing characteristics, and perception of fishermen about GRD conservation in the Narayani, Sapta Koshi, and Karnali rivers so conservation managers can develop and implement a potential solution to the GRD-fishery interaction problem in Nepal. Based on 169 interviews, 79% of Nepalese fishermen indicated fishing was their primary form of income. Fishermen reported fishing effort was greater in summer than winter; greatest in the afternoon (14:30 hrs ± 0:27) and during low water level conditions; and gear was set 4.8 ± 0.2 days/week. Fishermen reported using eight different types of monofilament nets (gillnets and cast nets). Sixty percent used gillnets less than 10 m long, and nearly 30% preferred gillnets between 10 and 100 m long; a few used gillnets longer than 100 m. Most fishermen reported they believed education, awareness, and changing occupations were important for GRD conservation, but they indicated that alternative occupational options were currently limited in Nepal. Nepalese fishermen acknowledged that fisheries posed a risk to GRD, but they believed water pollution, and dam/irrigation developments were the greatest threats. creator: Shambhu Paudel creator: Juan C. Levesque creator: Camilo Saavedra creator: Cristina Pita creator: Prabhat Pal uri: https://doi.org/10.7717/peerj.1563 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Paudel et al. title: Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective link: https://peerj.com/articles/1556 last-modified: 2016-01-12 description: The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers. creator: Rosa Alicia Jiménez creator: Juan Francisco Ornelas uri: https://doi.org/10.7717/peerj.1556 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Jiménez & Ornelas title: Molecular phylogeny and taxonomy of the Epictia goudotii Species complex (Serpentes: Leptotyphlopidae: Epictinae) in Middle America and northern South America link: https://peerj.com/articles/1551 last-modified: 2016-01-12 description: Here we review the systematics of the threadsnakes of the Epictia goudotii Species complex in Middle and northern South America using external morphology and molecular data. Two species, Epictia goudotii and E. magnamaculata, are currently recognized from that region, but we provide evidence for recognizing, as species, three other nominal forms usually treated as subspecies of E. goudotii: E. ater, E. bakewelli, and E. phenops. Thus, together with E. columbi (Bahamas), we recognize six species in the Epictia goudotii Species complex. Because E. albifrons from northern South America has been confused with E. goudotii in the past, we also briefly discuss the taxonomic status of that species and its apparent close relative E. tenella, which are not members of the E. goudotii complex. creator: James R. McCranie creator: S. Blair Hedges uri: https://doi.org/10.7717/peerj.1551 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 McCranie and Hedges title: Unveiling the status of alien animals in the arid zone of Asia link: https://peerj.com/articles/1545 last-modified: 2016-01-12 description: Biological invasion is one of the most threatening factors for biodiversity conservation. Lacking information on alien species in certain regions of the world hampers a balanced understanding of invasion processes and efficient data exchange among stakeholders. Current knowledge gaps are in need of urgent concern. We therefore conducted a review on alien animals in Xinjiang, an unknown region of invasion ecology. Xinjiang lies in the heartland of the Asian continent, covering an area of 1,664,900 km2. In the past 64 years, 128 alien animal species were recorded in this region, 39% of which became invasive and led to loss of native biodiversity. Most of these species were introduced through diversification of local agriculture and aquaculture. This process was aggravated by improving transportation and flourishing trade. Multiple linear regression models and correlation analysis were run for explaining influence of environmental and anthropogenic factors on status of alien animals: economically developed areas with abundant water resource, oases in particular, were prone to be hotspots of alien animal species in this arid and semi-arid region. This study also revealed that taxonomically biased and lagged research were critical problems that impeded studies on biological invasions in Xinjiang, and proposed feasible solutions. creator: Lyubing Zhang creator: Zhigang Jiang uri: https://doi.org/10.7717/peerj.1545 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhang and Jiang title: Fibroblast growth factors as tissue repair and regeneration therapeutics link: https://peerj.com/articles/1535 last-modified: 2016-01-12 description: Cell communication is central to the integration of cell function required for the development and homeostasis of multicellular animals. Proteins are an important currency of cell communication, acting locally (auto-, juxta-, or paracrine) or systemically (endocrine). The fibroblast growth factor (FGF) family contributes to the regulation of virtually all aspects of development and organogenesis, and after birth to tissue maintenance, as well as particular aspects of organism physiology. In the West, oncology has been the focus of translation of FGF research, whereas in China and to an extent Japan a major focus has been to use FGFs in repair and regeneration settings. These differences have their roots in research history and aims. The Chinese drive into biotechnology and the delivery of engineered clinical grade FGFs by a major Chinese research group were important enablers in this respect. The Chinese language clinical literature is not widely accessible. To put this into context, we provide the essential molecular and functional background to the FGF communication system covering FGF ligands, the heparan sulfate and Klotho co-receptors and FGF receptor (FGFR) tyrosine kinases. We then summarise a selection of clinical reports that demonstrate the efficacy of engineered recombinant FGF ligands in treating a wide range of conditions that require tissue repair/regeneration. Alongside, the functional reasons why application of exogenous FGF ligands does not lead to cancers are described. Together, this highlights that the FGF ligands represent a major opportunity for clinical translation that has been largely overlooked in the West. creator: Quentin M. Nunes creator: Yong Li creator: Changye Sun creator: Tarja K. Kinnunen creator: David G. Fernig uri: https://doi.org/10.7717/peerj.1535 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Nunes et al. title: Solid phase extraction and metabolic profiling of exudates from living copepods link: https://peerj.com/articles/1529 last-modified: 2016-01-12 description: Copepods are ubiquitous in aquatic habitats. They exude bioactive compounds that mediate mate finding or induce defensive traits in prey organisms. However, little is known about the chemical nature of the copepod exometabolome that contributes to the chemical landscape in pelagic habitats. Here we describe the development of a closed loop solid phase extraction setup that allows for extraction of exuded metabolites from live copepods. We captured exudates from male and female Temora longicornis and analyzed the content with high resolution LC-MS. Chemometric methods revealed 87 compounds that constitute a specific chemical pattern either qualitatively or quantitatively indicating copepod presence. The majority of the compounds were present in both female and male exudates, but nine compounds were mainly or exclusively present in female exudates and hence potential pheromone candidates. Copepodamide G, known to induce defensive responses in phytoplankton, was among the ten compounds of highest relative abundance in both male and female extracts. The presence of copepodamide G shows that the method can be used to capture and analyze chemical signals from living source organisms. We conclude that solid phase extraction in combination with metabolic profiling of exudates is a useful tool to develop our understanding of the chemical interplay between pelagic organisms. creator: Erik Selander creator: Jan Heuschele creator: Göran M. Nylund creator: Georg Pohnert creator: Henrik Pavia creator: Oda Bjærke creator: Larisa A. Pender-Healy creator: Peter Tiselius creator: Thomas Kiørboe uri: https://doi.org/10.7717/peerj.1529 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Selander et al. title: One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples link: https://peerj.com/articles/1560 last-modified: 2016-01-11 description: Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8–100% sensitivity, 99.7–100% specificity, 85–95% efficiency and a limit of detection of 4–60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81–92% efficiency and limit of detection of 150–600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8–100% sensitivity, 100% specificity, 86–89% efficiency and a limit of detection of 12–400 copies per singleplex reactions. The VP4 qRT-PCRs exhibited 82–90% efficiency and limit of detection of 120–4000 copies in multiplex reaction. Discussion. The one-step multiplex qRT-PCR assay will facilitate high-throughput rotavirus genotype characterization for monitoring circulating rotavirus wild-type strains causing rotavirus infections, determining the frequency of Rotarix® and RotaTeq® vaccine strains and vaccine-derived reassortants associated with AGE, and help to identify novel rotavirus strains derived by reassortment between vaccine and wild-type strains. creator: Rashi Gautam creator: Slavica Mijatovic-Rustempasic creator: Mathew D. Esona creator: Ka Ian Tam creator: Osbourne Quaye creator: Michael D. Bowen uri: https://doi.org/10.7717/peerj.1560 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: